16LN

Technical details

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library(GeoPressureR)
library(leaflet)
library(leaflet.extras)
library(raster)
library(dplyr)
library(ggplot2)
library(kableExtra)
library(plotly)
library(GeoLocTools)
setupGeolocation()
knitr::opts_chunk$set(echo = FALSE)
load(paste0("../data/1_pressure/", params$gdl_id, "_pressure_prob.Rdata"))
load(paste0("../data/2_light/", params$gdl_id, "_light_prob.Rdata"))
load(paste0("../data/3_static/", params$gdl_id, "_static_prob.Rdata"))
load(paste0("../data/4_basic_graph/", params$gdl_id, "_basic_graph.Rdata"))

Settings used

All the results produced here are generated with (1) the raw geolocator data, (2) the labeled files of pressure and light and (3) the parameters listed below.

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kable(gpr) %>% scroll_box(width = "100%")
gdl_id crop_start crop_end thr_dur extent_N extent_W extent_S extent_E map_scale map_max_sample map_margin prob_map_s prob_map_thr shift_k kernel_adjust calib_lon calib_lat calib_1_start calib_1_end calib_2_start calib_2_end calib_2_lon calib_2_lat prob_light_w thr_prob_percentile thr_gs RingNo scientific_name common_name mass wing_span Color
16LN 2017-02-10 2017-12-10 6 17 9 -25 38 5 300 30 1.2 0.9 0 1.4 28.76857 -22.72463 2017-02-10 2017-04-05 2017-11-19 2017-12-10 NA NA 0.1 0.95 120 NA Halcyon senegaloides Woodland Kingfisher NA NA #70D6FF

Pressure timeserie

The labeling of pressure data is illustrated with this figure. The black dots indicates the pressure datapoint not considered in the matching. Each stationary period is illustrated by a different colored line.

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pressure_na <- pam$pressure %>%
  mutate(obs = ifelse(isoutliar | sta_id == 0, NA, obs))
p <- ggplot() +
  geom_line(data = pam$pressure, aes(x = date, y = obs), colour = "grey") +
  geom_point(data = subset(pam$pressure, isoutliar), aes(x = date, y = obs), colour = "black") +
  # geom_line(data = pressure_na, aes(x = date, y = obs, color = factor(sta_id)), size = 0.5) +
  geom_line(data = do.call("rbind", shortest_path_timeserie) %>% filter(sta_id > 0), aes(x = date, y = pressure0, col = factor(sta_id))) +
  theme_bw() +
  scale_colour_manual(values = pam$sta$col) +
  scale_y_continuous(name = "Pressure(hPa)")

ggplotly(p, dynamicTicks = T) %>% layout(showlegend = F)

Pressure calibration

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sp_pressure = do.call("rbind", shortest_path_timeserie) %>% filter(sta_id > 0)

sta_plot <- which(difftime(pam$sta$end,pam$sta$start,unit="days")>3)

par(mfrow=c(2,3))
for (i in seq_len(length(sta_plot))){
  i_s = sta_plot[i]
  pressure_s = pam$pressure %>% 
    filter(sta_id==i_s & !isoutliar)
  
    err <- pressure_s %>% left_join(sp_pressure, by="date") %>% 
      mutate(
        err = obs-pressure-mean(obs-pressure)
      ) %>% .$err
    
    hist(err, freq = F, main = paste0("sta_id=",i_s, " | ",nrow(pressure_s)," dtpts | std=",round(sd(err),2)))
   xfit <- seq(min(err), max(err), length = 40) 
    yfit <- dnorm(xfit, mean = mean(err), sd = sd(err)) 
    lines(xfit, yfit, col = "red")
}

Light

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raw_geolight <- pam$light %>%
  transmute(
    Date = date,
    Light = obs
  )
lightImage(tagdata = raw_geolight, offset = 0)
tsimagePoints(twl$twilight,
  offset = 0, pch = 16, cex = 1.2,
  col = ifelse(twl$deleted, "grey20", ifelse(twl$rise, "firebrick", "cornflowerblue"))
)
abline(v = gpr$calib_2_start, lty = 1, col = "firebrick", lwd = 1.5)
abline(v = gpr$calib_1_start, lty = 1, col = "firebrick", lwd = 1.5)
abline(v = gpr$calib_2_end, lty = 2, col = "firebrick", lwd = 1.5)
abline(v = gpr$calib_1_end, lty = 2, col = "firebrick", lwd = 1.5)

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hist(z, freq = F)
lines(fit_z, col = "red")

The probability map resulting from light data alone can be seen below.

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li_s <- list()
l <- leaflet(width = "100%") %>%
  addProviderTiles(providers$Stamen.TerrainBackground) %>%
  addFullscreenControl()
for (i_r in seq_len(length(light_prob))) {
  i_s <- metadata(light_prob[[i_r]])$sta_id
  info <- pam$sta[pam$sta$sta_id == i_s, ]
  info_str <- paste0(i_s, " | ", info$start, "->", info$end)
  li_s <- append(li_s, info_str)
  l <- l %>% addRasterImage(light_prob[[i_r]], opacity = 0.8, colors = "OrRd", group = info_str)
}
l %>%
  addCircles(lng = gpr$calib_lon, lat = gpr$calib_lat, color = "black", opacity = 1) %>%
  addLayersControl(
    overlayGroups = li_s,
    options = layersControlOptions(collapsed = FALSE)
  ) %>%
  hideGroup(tail(li_s, length(li_s) - 1))

Light vs Pressure

We can compare light and pressure location at long stationary stopover (>5 days). By assuming the best match of the pressure to be the truth, we can plot the histogram of the zenith angle and compare to the fit of kernel density at the calibration site.

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 raw_geolight <- pam$light %>%
    transmute(
      Date = date,
      Light = obs
    )
 dur <- unlist(lapply(pressure_prob, function(x) difftime(metadata(x)$temporal_extent[2],metadata(x)$temporal_extent[1], units = "days" )))
  long_id <- which(dur>5)

par(mfrow = c(2, 3))
for (i_s in long_id){
  twl_fl <- twl %>%
    filter(!deleted) %>%
    filter(twilight>shortest_path_timeserie[[i_s]]$date[1] & twilight<tail(shortest_path_timeserie[[i_s]]$date,1))
  sun <-  solar(twl_fl$twilight)
  z_i <- refracted(zenith(sun, shortest_path_timeserie[[i_s]]$lon[1], shortest_path_timeserie[[i_s]]$lat[1]))
  hist(z_i, freq = F, main = paste0("sta_id=",i_s, " | ",nrow(twl_fl),"twls"))
  lines(fit_z, col = "red")
  xlab("Zenith angle")
}

Similarly, we can plot the line of sunrise/sunset at the best match of pressure (yellow line) and compare to the raw and labeled light data.

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  lightImage(
    tagdata = raw_geolight,
    offset = gpr$shift_k / 60 / 60
  )
  tsimagePoints(twl$twilight,
                offset = gpr$shift_k / 60 / 60, pch = 16, cex = 1.2,
                col = ifelse(twl$deleted, "grey20", ifelse(twl$rise, "firebrick", "cornflowerblue"))
  )
  for (ts in shortest_path_timeserie){
    if (!is.null(ts)){
      twl_fl <- twl %>%
      filter(twilight>ts$date[1] & twilight<tail(ts$date,1))
      if (nrow(twl_fl)>0){
      tsimageDeploymentLines(twl_fl$twilight,
                             lon = ts$lon[1], ts$lat[1],
                             offset = gpr$shift_k / 60 / 60, lwd = 3,col = adjustcolor("orange", alpha.f = 0.5))
        
      }
    }
  }

GeoPressureViz

To visualize the path on GeoPressureViz, you will need to also load the pressure and light probability map and align them first with the code below.

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sta_marginal <- unlist(lapply(static_prob_marginal, function(x) raster::metadata(x)$sta_id))
sta_pres <- unlist(lapply(pressure_prob, function(x) raster::metadata(x)$sta_id))
sta_light <- unlist(lapply(light_prob, function(x) raster::metadata(x)$sta_id))
pressure_prob <- pressure_prob[sta_pres %in% sta_marginal]
light_prob <- light_prob[sta_light %in% sta_marginal]

The code below will open with the shortest path computed with the graph approach.

Show code
geopressureviz <- list(
  pam_data = pam,
  static_prob = static_prob,
  static_prob_marginal = static_prob_marginal,
  pressure_prob = pressure_prob,
  light_prob = light_prob,
  pressure_timeserie = shortest_path_timeserie
)
save(geopressureviz, file = "~/geopressureviz.RData")

shiny::runApp(system.file("geopressureviz", package = "GeoPressureR"),
  launch.browser = getOption("browser")
)

Stationay period information

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pam$sta %>% mutate(duration = difftime(end,start,units="days")) %>% kable()
start end sta_id col duration
2017-02-10 00:00:00 2017-04-04 19:45:00 1 #1B9E77 53.8229167 days
2017-04-05 03:50:00 2017-04-05 17:40:00 2 #D95F02 0.5763889 days
2017-04-05 21:10:00 2017-04-06 01:05:00 3 #7570B3 0.1631944 days
2017-04-06 03:40:00 2017-04-06 23:55:00 4 #E7298A 0.8437500 days
2017-04-07 03:05:00 2017-04-07 18:20:00 5 #66A61E 0.6354167 days
2017-04-07 21:10:00 2017-04-08 17:40:00 6 #E6AB02 0.8541667 days
2017-04-08 22:15:00 2017-04-09 20:00:00 7 #A6761D 0.9062500 days
2017-04-10 03:05:00 2017-04-10 20:15:00 8 #666666 0.7152778 days
2017-04-10 20:55:00 2017-04-11 22:25:00 9 #1B9E77 1.0625000 days
2017-04-11 23:50:00 2017-04-14 21:10:00 10 #D95F02 2.8888889 days
2017-04-14 23:30:00 2017-04-20 19:25:00 11 #7570B3 5.8298611 days
2017-04-21 00:50:00 2017-04-21 19:10:00 12 #E7298A 0.7638889 days
2017-04-21 20:05:00 2017-04-28 17:10:00 13 #66A61E 6.8784722 days
2017-04-29 02:00:00 2017-04-29 19:55:00 14 #E6AB02 0.7465278 days
2017-04-30 00:30:00 2017-04-30 20:50:00 15 #A6761D 0.8472222 days
2017-05-01 00:40:00 2017-05-02 22:15:00 16 #666666 1.8993056 days
2017-05-03 01:20:00 2017-05-03 20:25:00 17 #1B9E77 0.7951389 days
2017-05-03 22:35:00 2017-05-06 02:50:00 18 #D95F02 2.1770833 days
2017-05-06 03:30:00 2017-05-06 23:25:00 19 #7570B3 0.8298611 days
2017-05-07 01:10:00 2017-05-07 17:45:00 20 #E7298A 0.6909722 days
2017-05-07 22:30:00 2017-05-09 20:30:00 21 #66A61E 1.9166667 days
2017-05-09 21:10:00 2017-05-09 21:30:00 22 #E6AB02 0.0138889 days
2017-05-09 21:50:00 2017-05-10 20:00:00 23 #A6761D 0.9236111 days
2017-05-10 21:10:00 2017-05-11 21:20:00 24 #666666 1.0069444 days
2017-05-11 22:55:00 2017-05-12 01:15:00 25 #1B9E77 0.0972222 days
2017-05-12 01:35:00 2017-06-03 20:55:00 26 #D95F02 22.8055556 days
2017-06-03 22:20:00 2017-06-04 01:15:00 27 #7570B3 0.1215278 days
2017-06-04 01:30:00 2017-06-06 22:20:00 28 #E7298A 2.8680556 days
2017-06-06 22:45:00 2017-06-07 21:15:00 29 #66A61E 0.9375000 days
2017-06-07 23:40:00 2017-10-26 17:05:00 30 #E6AB02 140.7256944 days
2017-10-27 03:40:00 2017-10-27 17:00:00 31 #A6761D 0.5555556 days
2017-10-28 01:40:00 2017-10-28 16:55:00 32 #666666 0.6354167 days
2017-10-28 23:30:00 2017-10-29 17:00:00 33 #1B9E77 0.7291667 days
2017-10-30 03:35:00 2017-10-30 17:50:00 34 #D95F02 0.5937500 days
2017-10-30 21:25:00 2017-10-30 23:50:00 35 #7570B3 0.1006944 days
2017-10-31 00:10:00 2017-10-31 18:50:00 36 #E7298A 0.7777778 days
2017-11-01 03:20:00 2017-11-01 21:40:00 37 #66A61E 0.7638889 days
2017-11-02 00:40:00 2017-11-03 22:50:00 38 #E6AB02 1.9236111 days
2017-11-04 01:15:00 2017-11-05 00:55:00 39 #A6761D 0.9861111 days
2017-11-05 02:50:00 2017-11-06 20:15:00 40 #666666 1.7256944 days
2017-11-06 21:25:00 2017-11-07 17:55:00 41 #1B9E77 0.8541667 days
2017-11-07 22:50:00 2017-11-08 20:25:00 42 #D95F02 0.8993056 days
2017-11-08 23:05:00 2017-11-13 17:35:00 43 #7570B3 4.7708333 days
2017-11-13 23:50:00 2017-11-15 18:40:00 44 #E7298A 1.7847222 days
2017-11-15 23:20:00 2017-11-16 17:55:00 45 #66A61E 0.7743056 days
2017-11-17 02:40:00 2017-11-17 17:25:00 46 #E6AB02 0.6145833 days
2017-11-17 21:35:00 2017-12-09 23:55:00 47 #A6761D 22.0972222 days